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The majority of human genomic research studies have been conducted in European-ancestry cohorts, reducing the likelihood of detecting potentially novel and globally impactful findings. Here, we present mid-pass whole-genome sequencing data and a genome-wide association study in a cohort of 264 self-reported Malagasy individuals from three locations on the island of Madagascar. We describe genetic variation in this Malagasy cohort, providing insight into the shared and unique patterns of genetic variation across the island. We observe phenotypic variation by location and find high rates of hypertension, particularly in the Southern Highlands sampling site, as well as elevated self-reported malaria prevalence in the West Coast site relative to other sites. After filtering to a subset of 214 minimally related individuals, we find a number of genetic associations with body composition traits, including many variants that are only observed in African populations or populations with admixed African ancestry from the 1000 Genomes Project. This study highlights the importance of including diverse populations in genomic research for the potential to gain novel insights, even with small cohort sizes. This project was conducted in partnership and consultation with local stakeholders in Madagascar and serves as an example of genomic research that prioritizes community engagement and potentially impacts our understanding of human health and disease., Competing Interests: Declaration of interests I.H., M.M., A.-K.E., M.H., S.L.v.B., K.A.W., L.Y.-A., and S.E.C. are employees and option or shareholders of Variant Bio, Inc.; K.A.W. and S.E.C. are co-founders of Variant Bio, Inc., and S.E.C. is a member of its board of directors. L.Y.-A. is a shareholder of GSK., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)